A multi-core R package that contains a set of tools based on copula graphical models for accomplishing the three interrelated goals in genetics and genomics in an unified way: (1) linkage map construction, (2) constructing linkage disequilibrium networks, and (3) exploring high-dimensional genotype-phenotype network and genotype- phenotype-environment interactions networks. The netgwas package can deal with biparental inbreeding and outbreeding species with any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes), tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where number of variables p is considerably larger than number of sample sizes (p >> n). The computations is memory-optimized using the sparse matrix output. The package is implemented the recent methodological developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287> and Behrouzi and Wit (2017) <doi:10.1093/bioinformatics/bty777>. NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
| Version: | 1.11 |
| Depends: | R (≥ 3.1.0) |
| Imports: | Matrix, igraph, qtl, parallel, methods, glasso, MASS, RBGL, huge, tmvtnorm |
| Suggests: | testthat |
| Published: | 2019-10-15 |
| Author: | Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit |
| Maintainer: | Pariya Behrouzi <pariya.behrouzi at gmail.com> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| Citation: | netgwas citation info |
| CRAN checks: | netgwas results |
| Reference manual: | netgwas.pdf |
| Package source: | netgwas_1.11.tar.gz |
| Windows binaries: | r-devel: netgwas_1.11.zip, r-release: netgwas_1.11.zip, r-oldrel: netgwas_1.11.zip |
| macOS binaries: | r-release: netgwas_1.11.tgz, r-oldrel: netgwas_1.11.tgz |
| Old sources: | netgwas archive |
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